No, that's literally the reason. If he finds out they're still together, then they believe he'll cut her off and not only mean she can't attend college anymore but she'll be lumbered with paying it back. Whether that's true or not remains to be seen, but he and his threat is literally the reason for the secrecy. The game makes that explicitly clear. You just can't accept anything other than believing their relationship is just rotten through and through to soothe your own mind when the truth is it's just in a difficult spot.
Again, DPC can't be expected to show us everything they get up to in their spare time. It's not relevant to show us what every character is doing at all times when it doesn't or won't directly involve the MC. We see Quinn stuff a lot but that's going to eventually impact him and it's pretty much the main plot of the game. But seeing Josy & Maya spending quality time together where it will have nothing to do with the MC or a main plotline is not relevant.
Also, we're not even seeing most of what the MC gets up to these days either so we have to assume things are going on there too, it's just less important than what we are seeing. The story, like all stories, is focusing on what's most important to see, and just because we skip a few weeks without seeing the MC with whatever girls he's with doesn't mean he isn't spending time with them, and just because we don't see or know about Josy & Maya spending time together doesn't mean they aren't either.
